|
| Status |
Public on Feb 12, 2024 |
| Title |
WT_RNAseq_Day4_Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Colon
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Colon
cell line: HCT116
cell type: Colorectal cancer cell
treatment: Auxin treatment for 4 days
|
| Treatment protocol |
To facilitate the auxin treatment, HCT116 cells were cultured in a medium supplemented with 2 μg/mL doxycycline and 20 μM auxinole for a duration of one day. Subsequently, the cells were maintained in a medium containing 2 μg/mL doxycycline and 500 μM auxin. During the course of the auxin treatment, the medium was refreshed every two days to ensure a consistent concentration of doxycycline and auxin throughout the experimental period.
|
| Growth protocol |
HCT116 cells were maintained in McCoy’s 5A medium with L-glutamine supplemented with 10% FBS and 1% Penicillin/Streptomycin.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was isolated using the RNAeasy Plus Mini Kit (Qiagen) according to the manufacturer's protocol.
The library preparation for RNA-seq was performed by Novogene company. mRNA-seq libraries were prepared by NEB Next® Ultra™ RNA Library Prep Kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
RNA-Seq reads were processed using STAR.https://github.com/alexdobin/STAR.
read counts from featureCounts.
Genome_build: hg38
Assembly: hg38
Supplementary files format and content: Processed data files were obtained with above data processing steps. Supplementary files format and content: read counts
|
| |
|
| Submission date |
Dec 06, 2023 |
| Last update date |
Feb 12, 2024 |
| Contact name |
Pierre-Antoine Defossez |
| E-mail(s) |
[email protected]
|
| Organization name |
Epigenetics and Cell Fate Unit
|
| Street address |
35 rue Hélène Brion
|
| City |
Paris |
| ZIP/Postal code |
75013 |
| Country |
France |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE249536 |
Non-canonical functions of UHRF1 maintain DNA methylation homeostasis in cancer cells [RNA-seq] |
|
| Relations |
| BioSample |
SAMN38700103 |
| SRA |
SRX22806760 |
